MAPK11 p.Cys39=
c.117T>C · VCV4103720
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0762%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 16.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0762%
African / African-American · 54/70,820 alleles
Filtering AF
0.0599%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.00379%
59/1,558,756 alleles · ultra-rare
exomes 30/1,406,498 · genomes 29/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0762% | 1,311 |
| Admixed American | 0.00554% | 18,047 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 30,068 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MAPK11
- Protein
- p.Cys39=
- Coding
- c.117T>C
- MANE Select
- NM_002751
- Type
- single nucleotide variant
- Location
- chr22:50267949 (GRCh38)
- Gene constraint
- LOEUF 1.307 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.88 · 4 PDB
- Residue 39
- the protein kinase domain; a β-strand
Similar variants
- MAPK11 c.611-7C>T Benign ★★ same type
- MAPK11 p.Ala121Ser Uncertain significance ★ ⚠ same type
- MAPK11 p.Ala184Thr Uncertain significance ★ ⚠ same type
- MAPK11 p.Ala304Ser Uncertain significance ★ ⚠ same type
- MAPK11 p.Arg189Gln Uncertain significance ★ ⚠ same type
- MAPK11 p.Arg332His Uncertain significance ★ ⚠ same type
- MAPK11 p.Arg45Trp Uncertain significance ★ ⚠ same type
- MAPK11 p.Asp161Asn Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mapk11-p-cys39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown